Starting phenix.real_space_refine on Fri Mar 6 15:45:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ws1_32740/03_2026/7ws1_32740_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ws1_32740/03_2026/7ws1_32740.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ws1_32740/03_2026/7ws1_32740.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ws1_32740/03_2026/7ws1_32740.map" model { file = "/net/cci-nas-00/data/ceres_data/7ws1_32740/03_2026/7ws1_32740_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ws1_32740/03_2026/7ws1_32740_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 142 5.16 5 C 20439 2.51 5 N 5280 2.21 5 O 6351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32212 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 8060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8060 Classifications: {'peptide': 1041} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 52, 'TRANS': 988} Chain breaks: 7 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 2, 'GLN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "B" Number of atoms: 8039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8039 Classifications: {'peptide': 1038} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 52, 'TRANS': 985} Chain breaks: 7 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 3, 'GLN:plan1': 2, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "C" Number of atoms: 8053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1039, 8053 Classifications: {'peptide': 1039} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 52, 'TRANS': 986} Chain breaks: 7 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 3, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "D" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 967 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "H" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 967 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "F" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 967 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "J" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 967 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 7.64, per 1000 atoms: 0.24 Number of scatterers: 32212 At special positions: 0 Unit cell: (143.5, 173.84, 238.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 142 16.00 O 6351 8.00 N 5280 7.00 C 20439 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " NAG-ASN " NAG A1301 " - " ASN A 165 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 61 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 165 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 61 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 165 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 61 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG L 1 " - " ASN A 343 " " NAG M 1 " - " ASN A 717 " " NAG N 1 " - " ASN A 801 " " NAG O 1 " - " ASN A 17 " " NAG P 1 " - " ASN A1098 " " NAG Q 1 " - " ASN A1134 " " NAG R 1 " - " ASN B 17 " " NAG S 1 " - " ASN B 343 " " NAG T 1 " - " ASN B 717 " " NAG U 1 " - " ASN B 801 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN B1134 " " NAG X 1 " - " ASN C 17 " " NAG Y 1 " - " ASN C 343 " " NAG Z 1 " - " ASN C 717 " " NAG a 1 " - " ASN C 801 " " NAG b 1 " - " ASN C1098 " " NAG c 1 " - " ASN C1134 " Time building additional restraints: 2.78 Conformation dependent library (CDL) restraints added in 1.3 seconds 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7548 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 78 sheets defined 19.5% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.923A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.701A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.585A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 748 through 754 removed outlier: 3.504A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 760 through 783 removed outlier: 4.059A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.588A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.985A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.673A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.218A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.865A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.190A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 3.521A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.678A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.619A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.718A pdb=" N GLN B 409 " --> pdb=" O GLU B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.585A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 752 removed outlier: 3.817A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 removed outlier: 4.214A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 826 removed outlier: 3.820A pdb=" N PHE B 823 " --> pdb=" O GLU B 819 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.961A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.775A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.340A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.903A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.133A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.048A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.548A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.683A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.988A pdb=" N ALA C 766 " --> pdb=" O GLN C 762 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.597A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.549A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.962A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.758A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.565A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.921A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.686A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.255A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.888A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.579A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'I' and resid 62 through 65 removed outlier: 3.579A pdb=" N LYS I 65 " --> pdb=" O ASP I 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 62 through 65' Processing helix chain 'G' and resid 62 through 65 removed outlier: 3.580A pdb=" N LYS G 65 " --> pdb=" O ASP G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'K' and resid 28 through 32 removed outlier: 4.055A pdb=" N ASP K 31 " --> pdb=" O THR K 28 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 28 through 32' Processing helix chain 'K' and resid 62 through 65 Processing helix chain 'K' and resid 87 through 91 removed outlier: 4.010A pdb=" N THR K 91 " --> pdb=" O ALA K 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.717A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.747A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.715A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.828A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 132 through 142 removed outlier: 6.742A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N CYS A 136 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.992A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.085A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 316 removed outlier: 6.843A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.657A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 5.941A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 538 through 540 Processing sheet with id=AB3, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.768A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.264A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.584A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 712 through 722 removed outlier: 6.476A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 725 through 728 Processing sheet with id=AB8, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.218A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.546A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.629A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.839A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.892A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.108A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 132 through 134 removed outlier: 3.996A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 140 through 142 removed outlier: 3.909A pdb=" N PHE B 140 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.072A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.139A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.879A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 573 through 575 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.093A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 9.005A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD6, first strand: chain 'B' and resid 712 through 722 removed outlier: 6.675A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 712 through 722 removed outlier: 6.675A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.332A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.300A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.563A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 10.125A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.563A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE5, first strand: chain 'C' and resid 132 through 135 removed outlier: 3.740A pdb=" N GLU C 132 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASN C 164 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.223A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.838A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 361 through 362 removed outlier: 5.806A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF2, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.759A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 542 through 543 removed outlier: 3.662A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.523A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.681A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AF7, first strand: chain 'C' and resid 1086 through 1090 removed outlier: 4.702A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF9, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AG1, first strand: chain 'D' and resid 10 through 13 removed outlier: 5.555A pdb=" N LEU D 11 " --> pdb=" O GLU D 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.796A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR D 98 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.878A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AG5, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.716A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 4 through 6 removed outlier: 4.200A pdb=" N ASP H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER H 67 " --> pdb=" O ASP H 70 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 10 through 13 removed outlier: 5.555A pdb=" N LEU H 11 " --> pdb=" O GLU H 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'H' and resid 53 through 54 removed outlier: 6.797A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR H 98 " --> pdb=" O GLN H 90 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.878A pdb=" N SER I 21 " --> pdb=" O SER I 7 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'I' and resid 11 through 12 Processing sheet with id=AH2, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.716A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLY I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N MET I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 4 through 6 removed outlier: 4.201A pdb=" N ASP F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER F 67 " --> pdb=" O ASP F 70 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 10 through 13 removed outlier: 5.554A pdb=" N LEU F 11 " --> pdb=" O GLU F 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.796A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR F 98 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.879A pdb=" N SER G 21 " --> pdb=" O SER G 7 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 11 through 12 Processing sheet with id=AH8, first strand: chain 'G' and resid 58 through 60 removed outlier: 6.716A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLY G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N MET G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 4 through 6 removed outlier: 3.764A pdb=" N VAL J 19 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASP J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.043A pdb=" N LEU J 11 " --> pdb=" O GLU J 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI1 Processing sheet with id=AI2, first strand: chain 'J' and resid 53 through 54 removed outlier: 6.936A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN J 90 " --> pdb=" O THR J 98 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR J 98 " --> pdb=" O GLN J 90 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.826A pdb=" N SER K 21 " --> pdb=" O SER K 7 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR K 80 " --> pdb=" O SER K 71 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'K' and resid 11 through 12 Processing sheet with id=AI5, first strand: chain 'K' and resid 58 through 60 removed outlier: 6.660A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLY K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N MET K 34 " --> pdb=" O GLY K 50 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR K 112 " --> pdb=" O LYS K 98 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'K' and resid 58 through 60 removed outlier: 6.660A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLY K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N MET K 34 " --> pdb=" O GLY K 50 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR K 94 " --> pdb=" O THR K 117 " (cutoff:3.500A) 1135 hydrogen bonds defined for protein. 3069 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.81 Time building geometry restraints manager: 3.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10249 1.34 - 1.46: 7827 1.46 - 1.58: 14671 1.58 - 1.70: 0 1.70 - 1.82: 184 Bond restraints: 32931 Sorted by residual: bond pdb=" N ASP B 442 " pdb=" CA ASP B 442 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.18e-02 7.18e+03 1.05e+01 bond pdb=" N ASP I 31 " pdb=" CA ASP I 31 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.19e-02 7.06e+03 1.03e+01 bond pdb=" N ASP G 31 " pdb=" CA ASP G 31 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.19e-02 7.06e+03 1.00e+01 bond pdb=" N ASP C 442 " pdb=" CA ASP C 442 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.18e-02 7.18e+03 9.88e+00 bond pdb=" N ASP E 31 " pdb=" CA ASP E 31 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.19e-02 7.06e+03 9.83e+00 ... (remaining 32926 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 42659 1.35 - 2.69: 1763 2.69 - 4.04: 332 4.04 - 5.39: 46 5.39 - 6.73: 14 Bond angle restraints: 44814 Sorted by residual: angle pdb=" C THR D 69 " pdb=" N ASP D 70 " pdb=" CA ASP D 70 " ideal model delta sigma weight residual 122.87 116.84 6.03 1.61e+00 3.86e-01 1.40e+01 angle pdb=" C GLN A 506 " pdb=" N PRO A 507 " pdb=" CA PRO A 507 " ideal model delta sigma weight residual 119.78 123.13 -3.35 1.03e+00 9.43e-01 1.06e+01 angle pdb=" C ASP D 70 " pdb=" CA ASP D 70 " pdb=" CB ASP D 70 " ideal model delta sigma weight residual 109.37 115.17 -5.80 1.83e+00 2.99e-01 1.01e+01 angle pdb=" N TYR I 102 " pdb=" CA TYR I 102 " pdb=" C TYR I 102 " ideal model delta sigma weight residual 114.31 110.28 4.03 1.29e+00 6.01e-01 9.77e+00 angle pdb=" N TYR E 102 " pdb=" CA TYR E 102 " pdb=" C TYR E 102 " ideal model delta sigma weight residual 114.31 110.30 4.01 1.29e+00 6.01e-01 9.69e+00 ... (remaining 44809 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.97: 19080 21.97 - 43.93: 1083 43.93 - 65.90: 165 65.90 - 87.87: 57 87.87 - 109.84: 7 Dihedral angle restraints: 20392 sinusoidal: 8643 harmonic: 11749 Sorted by residual: dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 -173.64 87.64 1 1.00e+01 1.00e-02 9.21e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 177.03 -84.03 1 1.00e+01 1.00e-02 8.60e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -2.74 -83.26 1 1.00e+01 1.00e-02 8.47e+01 ... (remaining 20389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 5209 0.138 - 0.275: 28 0.275 - 0.413: 3 0.413 - 0.550: 2 0.550 - 0.688: 2 Chirality restraints: 5244 Sorted by residual: chirality pdb=" C1 NAG c 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG c 1 " pdb=" O5 NAG c 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" C1 NAG Y 1 " pdb=" ND2 ASN C 343 " pdb=" C2 NAG Y 1 " pdb=" O5 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.14e+00 chirality pdb=" C1 NAG C1305 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1305 " pdb=" O5 NAG C1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.49e+00 ... (remaining 5241 not shown) Planarity restraints: 5763 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B1074 " 0.155 2.00e-02 2.50e+03 1.99e-01 4.94e+02 pdb=" CG ASN B1074 " -0.063 2.00e-02 2.50e+03 pdb=" OD1 ASN B1074 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN B1074 " -0.338 2.00e-02 2.50e+03 pdb=" C1 NAG B1310 " 0.235 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 874 " -0.015 2.00e-02 2.50e+03 3.00e-02 9.00e+00 pdb=" C THR C 874 " 0.052 2.00e-02 2.50e+03 pdb=" O THR C 874 " -0.019 2.00e-02 2.50e+03 pdb=" N SER C 875 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 961 " -0.015 2.00e-02 2.50e+03 3.00e-02 8.98e+00 pdb=" C THR B 961 " 0.052 2.00e-02 2.50e+03 pdb=" O THR B 961 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU B 962 " -0.018 2.00e-02 2.50e+03 ... (remaining 5760 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5853 2.77 - 3.31: 28984 3.31 - 3.84: 50360 3.84 - 4.37: 56715 4.37 - 4.90: 102858 Nonbonded interactions: 244770 Sorted by model distance: nonbonded pdb=" NE2 GLN C 804 " pdb=" OE1 GLN C 935 " model vdw 2.244 3.120 nonbonded pdb=" OG SER A 721 " pdb=" OG1 THR A1066 " model vdw 2.244 3.040 nonbonded pdb=" OG1 THR B 323 " pdb=" NZ LYS B 537 " model vdw 2.257 3.120 nonbonded pdb=" ND2 ASN C1125 " pdb=" OD2 ASP C1127 " model vdw 2.258 3.120 nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.259 3.040 ... (remaining 244765 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 527 or (resid 528 through 532 and (name N or na \ me CA or name C or name O or name CB )) or resid 533 through 553 or (resid 554 a \ nd (name N or name CA or name C or name O or name CB )) or resid 555 or (resid 5 \ 56 and (name N or name CA or name C or name O or name CB )) or resid 557 through \ 827 or resid 854 through 984 or (resid 985 and (name N or name CA or name C or \ name O or name CB )) or resid 986 through 1044 or (resid 1045 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1046 through 1310)) selection = (chain 'B' and (resid 15 through 555 or (resid 556 and (name N or name CA or nam \ e C or name O or name CB )) or resid 557 or (resid 558 through 559 and (name N o \ r name CA or name C or name O or name CB )) or resid 560 through 613 or (resid 6 \ 14 and (name N or name CA or name C or name O or name CB )) or resid 615 through \ 785 or (resid 786 and (name N or name CA or name C or name O or name CB )) or r \ esid 787 through 827 or (resid 854 and (name N or name CA or name C or name O or \ name CB )) or resid 855 through 903 or (resid 904 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ )) or resid 905 through 1044 or (resid 1045 and (name N or name C \ A or name C or name O or name CB )) or resid 1046 through 1310)) selection = (chain 'C' and (resid 15 through 527 or (resid 528 through 532 and (name N or na \ me CA or name C or name O or name CB )) or resid 533 through 553 or (resid 554 a \ nd (name N or name CA or name C or name O or name CB )) or resid 555 through 557 \ or (resid 558 through 559 and (name N or name CA or name C or name O or name CB \ )) or resid 560 through 613 or (resid 614 and (name N or name CA or name C or n \ ame O or name CB )) or resid 615 through 827 or resid 854 through 903 or (resid \ 904 and (name N or name CA or name C or name O or name CB or name CG or name CD1 \ or name CD2 or name CE1 or name CE2 or name CZ )) or resid 905 through 984 or ( \ resid 985 and (name N or name CA or name C or name O or name CB )) or resid 986 \ through 1310)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 32.180 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 33041 Z= 0.207 Angle : 0.665 20.274 45100 Z= 0.346 Chirality : 0.048 0.688 5244 Planarity : 0.004 0.053 5715 Dihedral : 13.841 109.837 12712 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.03 % Allowed : 0.26 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.13), residues: 3986 helix: 1.43 (0.22), residues: 647 sheet: -0.47 (0.15), residues: 1188 loop : -1.25 (0.13), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 357 TYR 0.023 0.001 TYR J 92 PHE 0.021 0.001 PHE C 759 TRP 0.023 0.001 TRP A 64 HIS 0.002 0.000 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00369 (32931) covalent geometry : angle 0.62529 (44814) SS BOND : bond 0.00248 ( 44) SS BOND : angle 0.97673 ( 88) hydrogen bonds : bond 0.17742 ( 1118) hydrogen bonds : angle 7.86791 ( 3069) link_BETA1-4 : bond 0.00448 ( 18) link_BETA1-4 : angle 1.89007 ( 54) link_NAG-ASN : bond 0.00544 ( 48) link_NAG-ASN : angle 3.87395 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 473 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 572 THR cc_start: 0.7861 (m) cc_final: 0.7605 (m) REVERT: C 153 MET cc_start: 0.3937 (ppp) cc_final: 0.2697 (tmm) REVERT: C 197 ILE cc_start: 0.8419 (mm) cc_final: 0.7864 (mp) REVERT: C 584 ILE cc_start: 0.8962 (mm) cc_final: 0.8570 (mm) REVERT: C 796 ASP cc_start: 0.6867 (p0) cc_final: 0.6546 (p0) REVERT: C 814 LYS cc_start: 0.8061 (mmmt) cc_final: 0.7816 (mmmt) REVERT: F 5 THR cc_start: 0.5367 (p) cc_final: 0.4750 (p) outliers start: 1 outliers final: 0 residues processed: 474 average time/residue: 0.2093 time to fit residues: 159.5499 Evaluate side-chains 293 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.0770 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.0170 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 overall best weight: 2.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 439 ASN A 774 GLN A 907 ASN B 81 ASN B 439 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 ASN D 6 GLN D 34 ASN H 34 ASN H 38 HIS H 89 GLN ** J 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 101 GLN ** K 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.103434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.064617 restraints weight = 84111.654| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 3.78 r_work: 0.2874 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 33041 Z= 0.196 Angle : 0.647 14.058 45100 Z= 0.327 Chirality : 0.047 0.482 5244 Planarity : 0.004 0.054 5715 Dihedral : 7.335 86.604 5732 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.31 % Allowed : 8.12 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.13), residues: 3986 helix: 1.83 (0.22), residues: 644 sheet: -0.19 (0.15), residues: 1111 loop : -1.37 (0.12), residues: 2231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 61 TYR 0.020 0.002 TYR D 49 PHE 0.019 0.002 PHE A 906 TRP 0.018 0.002 TRP B 353 HIS 0.005 0.001 HIS F 38 Details of bonding type rmsd covalent geometry : bond 0.00462 (32931) covalent geometry : angle 0.62164 (44814) SS BOND : bond 0.00398 ( 44) SS BOND : angle 1.10394 ( 88) hydrogen bonds : bond 0.04989 ( 1118) hydrogen bonds : angle 5.96816 ( 3069) link_BETA1-4 : bond 0.00546 ( 18) link_BETA1-4 : angle 1.59605 ( 54) link_NAG-ASN : bond 0.00450 ( 48) link_NAG-ASN : angle 3.04707 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 310 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8942 (p) cc_final: 0.8715 (t) REVERT: A 869 MET cc_start: 0.8934 (mtt) cc_final: 0.8703 (mtp) REVERT: A 1029 MET cc_start: 0.9433 (tpp) cc_final: 0.8991 (ttm) REVERT: C 153 MET cc_start: 0.4413 (ppp) cc_final: 0.3302 (tmm) REVERT: C 796 ASP cc_start: 0.8009 (p0) cc_final: 0.7396 (p0) REVERT: E 76 LYS cc_start: 0.8752 (tmmt) cc_final: 0.8432 (tmmt) REVERT: E 87 ARG cc_start: 0.7394 (ptp-110) cc_final: 0.6419 (ptp90) REVERT: E 99 ASP cc_start: 0.8943 (t70) cc_final: 0.8617 (t0) REVERT: H 79 GLN cc_start: 0.9176 (tp40) cc_final: 0.8906 (tp40) REVERT: H 87 TYR cc_start: 0.7823 (m-80) cc_final: 0.7539 (m-10) REVERT: H 104 LYS cc_start: 0.8932 (tppt) cc_final: 0.8717 (tptp) REVERT: H 105 LEU cc_start: 0.8694 (tt) cc_final: 0.8122 (tp) REVERT: F 37 GLN cc_start: 0.8607 (tt0) cc_final: 0.8315 (tm-30) REVERT: F 39 LYS cc_start: 0.8709 (mmmt) cc_final: 0.8346 (mmmt) REVERT: G 29 PHE cc_start: 0.7474 (t80) cc_final: 0.7145 (t80) REVERT: G 104 ILE cc_start: 0.8489 (tp) cc_final: 0.8029 (mp) REVERT: J 37 GLN cc_start: 0.8044 (tp-100) cc_final: 0.7607 (tp-100) REVERT: J 39 LYS cc_start: 0.8618 (pttt) cc_final: 0.8278 (ptmm) REVERT: J 45 LYS cc_start: 0.9105 (ptmt) cc_final: 0.8808 (mmmt) REVERT: K 82 GLN cc_start: 0.5038 (mm110) cc_final: 0.4629 (mm-40) REVERT: K 83 MET cc_start: 0.9130 (OUTLIER) cc_final: 0.8919 (mpp) outliers start: 45 outliers final: 31 residues processed: 335 average time/residue: 0.2036 time to fit residues: 110.1444 Evaluate side-chains 302 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 270 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 152 TRP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 95 TYR Chi-restraints excluded: chain K residue 110 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 173 optimal weight: 3.9990 chunk 14 optimal weight: 0.0370 chunk 0 optimal weight: 30.0000 chunk 245 optimal weight: 5.9990 chunk 221 optimal weight: 10.0000 chunk 270 optimal weight: 0.8980 chunk 227 optimal weight: 8.9990 chunk 151 optimal weight: 10.0000 chunk 296 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 315 optimal weight: 0.6980 overall best weight: 1.7262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN H 37 GLN ** J 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.102743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.063949 restraints weight = 84138.235| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 3.79 r_work: 0.2860 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 33041 Z= 0.165 Angle : 0.599 12.908 45100 Z= 0.300 Chirality : 0.046 0.460 5244 Planarity : 0.004 0.055 5715 Dihedral : 6.531 66.921 5732 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.69 % Allowed : 10.36 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.13), residues: 3986 helix: 1.90 (0.22), residues: 655 sheet: -0.12 (0.15), residues: 1123 loop : -1.33 (0.12), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 16 TYR 0.021 0.001 TYR G 112 PHE 0.017 0.001 PHE K 68 TRP 0.017 0.001 TRP K 113 HIS 0.008 0.001 HIS J 38 Details of bonding type rmsd covalent geometry : bond 0.00389 (32931) covalent geometry : angle 0.57282 (44814) SS BOND : bond 0.00359 ( 44) SS BOND : angle 1.04238 ( 88) hydrogen bonds : bond 0.04751 ( 1118) hydrogen bonds : angle 5.57420 ( 3069) link_BETA1-4 : bond 0.00469 ( 18) link_BETA1-4 : angle 1.61876 ( 54) link_NAG-ASN : bond 0.00431 ( 48) link_NAG-ASN : angle 2.95788 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 281 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8979 (p) cc_final: 0.8713 (t) REVERT: A 869 MET cc_start: 0.8949 (mtt) cc_final: 0.8721 (mtp) REVERT: A 979 ASP cc_start: 0.8766 (t70) cc_final: 0.8390 (t0) REVERT: B 52 GLN cc_start: 0.9115 (tt0) cc_final: 0.8868 (tm-30) REVERT: C 153 MET cc_start: 0.4500 (ppp) cc_final: 0.3441 (tmm) REVERT: C 796 ASP cc_start: 0.7998 (p0) cc_final: 0.7459 (p0) REVERT: D 81 GLU cc_start: 0.8808 (pp20) cc_final: 0.8569 (pp20) REVERT: E 76 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8535 (tmmt) REVERT: E 87 ARG cc_start: 0.7684 (ptp-110) cc_final: 0.6399 (ptp90) REVERT: E 99 ASP cc_start: 0.8996 (t70) cc_final: 0.8702 (t0) REVERT: H 4 MET cc_start: 0.7685 (tpp) cc_final: 0.7469 (tpp) REVERT: H 11 LEU cc_start: 0.8557 (tp) cc_final: 0.8050 (pt) REVERT: H 47 LEU cc_start: 0.8814 (mm) cc_final: 0.8544 (mm) REVERT: H 87 TYR cc_start: 0.7774 (m-80) cc_final: 0.7527 (m-10) REVERT: G 29 PHE cc_start: 0.7505 (t80) cc_final: 0.7098 (t80) REVERT: G 95 TYR cc_start: 0.6477 (OUTLIER) cc_final: 0.5099 (m-80) REVERT: G 100 ARG cc_start: 0.7615 (ttm110) cc_final: 0.7226 (tpp80) REVERT: G 104 ILE cc_start: 0.8397 (tp) cc_final: 0.8024 (mp) REVERT: J 39 LYS cc_start: 0.8650 (pttt) cc_final: 0.8429 (ptmm) REVERT: J 45 LYS cc_start: 0.9168 (ptmt) cc_final: 0.8923 (mmmt) REVERT: K 47 TRP cc_start: 0.4077 (t60) cc_final: 0.3493 (t60) REVERT: K 82 GLN cc_start: 0.4840 (mm110) cc_final: 0.4103 (mm-40) REVERT: K 83 MET cc_start: 0.9044 (mpp) cc_final: 0.8738 (mpp) REVERT: K 84 ASN cc_start: 0.8012 (m110) cc_final: 0.7262 (p0) outliers start: 58 outliers final: 36 residues processed: 318 average time/residue: 0.2018 time to fit residues: 103.5231 Evaluate side-chains 293 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 255 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 152 TRP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 95 TYR Chi-restraints excluded: chain G residue 110 PHE Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain K residue 95 TYR Chi-restraints excluded: chain K residue 110 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 350 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 266 optimal weight: 0.0980 chunk 11 optimal weight: 0.0980 chunk 15 optimal weight: 6.9990 chunk 381 optimal weight: 50.0000 chunk 298 optimal weight: 0.9980 chunk 192 optimal weight: 0.7980 chunk 389 optimal weight: 7.9990 chunk 227 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN B 81 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN J 34 ASN ** K 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.103222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.064542 restraints weight = 83615.966| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.80 r_work: 0.2872 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33041 Z= 0.120 Angle : 0.568 12.549 45100 Z= 0.283 Chirality : 0.045 0.445 5244 Planarity : 0.003 0.054 5715 Dihedral : 5.851 56.036 5732 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.83 % Allowed : 11.78 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.13), residues: 3986 helix: 2.07 (0.22), residues: 654 sheet: 0.01 (0.16), residues: 1095 loop : -1.30 (0.12), residues: 2237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 16 TYR 0.020 0.001 TYR B1067 PHE 0.020 0.001 PHE F 36 TRP 0.019 0.001 TRP K 113 HIS 0.012 0.001 HIS J 38 Details of bonding type rmsd covalent geometry : bond 0.00277 (32931) covalent geometry : angle 0.54147 (44814) SS BOND : bond 0.00255 ( 44) SS BOND : angle 0.89210 ( 88) hydrogen bonds : bond 0.04226 ( 1118) hydrogen bonds : angle 5.32248 ( 3069) link_BETA1-4 : bond 0.00478 ( 18) link_BETA1-4 : angle 1.63719 ( 54) link_NAG-ASN : bond 0.00428 ( 48) link_NAG-ASN : angle 2.85358 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 280 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8983 (p) cc_final: 0.8706 (t) REVERT: A 869 MET cc_start: 0.8988 (mtt) cc_final: 0.8571 (mtm) REVERT: A 979 ASP cc_start: 0.8769 (t70) cc_final: 0.8381 (t0) REVERT: B 505 TYR cc_start: 0.5931 (t80) cc_final: 0.5312 (t80) REVERT: C 153 MET cc_start: 0.4503 (ppp) cc_final: 0.3472 (tmm) REVERT: C 584 ILE cc_start: 0.8869 (mm) cc_final: 0.8311 (mm) REVERT: C 796 ASP cc_start: 0.8017 (p0) cc_final: 0.7495 (p0) REVERT: C 935 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8166 (tm-30) REVERT: D 81 GLU cc_start: 0.8806 (pp20) cc_final: 0.8415 (pp20) REVERT: E 76 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8661 (tmmt) REVERT: E 87 ARG cc_start: 0.7690 (ptp-110) cc_final: 0.6259 (ptp90) REVERT: E 99 ASP cc_start: 0.8985 (t70) cc_final: 0.8713 (t0) REVERT: E 111 ASP cc_start: 0.8609 (t0) cc_final: 0.8391 (t0) REVERT: E 112 TYR cc_start: 0.8603 (m-80) cc_final: 0.8332 (m-80) REVERT: H 18 ARG cc_start: 0.7787 (ttp80) cc_final: 0.7522 (ttp80) REVERT: H 39 LYS cc_start: 0.8537 (tppt) cc_final: 0.8217 (mmtp) REVERT: H 47 LEU cc_start: 0.8908 (mm) cc_final: 0.8584 (mm) REVERT: H 49 TYR cc_start: 0.8056 (p90) cc_final: 0.7703 (p90) REVERT: H 87 TYR cc_start: 0.7814 (m-80) cc_final: 0.7567 (m-10) REVERT: I 103 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8552 (mm-30) REVERT: G 29 PHE cc_start: 0.7498 (t80) cc_final: 0.7063 (t80) REVERT: G 95 TYR cc_start: 0.6528 (OUTLIER) cc_final: 0.5020 (m-80) REVERT: J 37 GLN cc_start: 0.7795 (tp-100) cc_final: 0.7588 (tp40) REVERT: J 38 HIS cc_start: 0.7314 (m170) cc_final: 0.7020 (m170) REVERT: K 47 TRP cc_start: 0.3849 (t60) cc_final: 0.3273 (t60) REVERT: K 68 PHE cc_start: 0.7750 (m-80) cc_final: 0.7029 (m-80) REVERT: K 82 GLN cc_start: 0.4839 (mm110) cc_final: 0.4299 (mm-40) REVERT: K 84 ASN cc_start: 0.8013 (m110) cc_final: 0.7260 (p0) outliers start: 63 outliers final: 44 residues processed: 324 average time/residue: 0.2060 time to fit residues: 108.5079 Evaluate side-chains 303 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 256 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 59 ASP Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 83 PHE Chi-restraints excluded: chain F residue 88 CYS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 95 TYR Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain K residue 110 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 172 optimal weight: 0.9990 chunk 203 optimal weight: 5.9990 chunk 334 optimal weight: 0.0170 chunk 220 optimal weight: 7.9990 chunk 112 optimal weight: 8.9990 chunk 254 optimal weight: 0.8980 chunk 118 optimal weight: 0.5980 chunk 380 optimal weight: 0.5980 chunk 70 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 328 optimal weight: 1.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.103754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.065266 restraints weight = 83479.031| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.78 r_work: 0.2889 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 33041 Z= 0.104 Angle : 0.558 12.266 45100 Z= 0.277 Chirality : 0.045 0.438 5244 Planarity : 0.003 0.053 5715 Dihedral : 5.329 53.497 5732 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.01 % Allowed : 12.89 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.13), residues: 3986 helix: 2.28 (0.22), residues: 647 sheet: 0.22 (0.16), residues: 1055 loop : -1.26 (0.12), residues: 2284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 16 TYR 0.019 0.001 TYR B1067 PHE 0.014 0.001 PHE F 36 TRP 0.026 0.001 TRP K 113 HIS 0.004 0.001 HIS J 38 Details of bonding type rmsd covalent geometry : bond 0.00238 (32931) covalent geometry : angle 0.53269 (44814) SS BOND : bond 0.00352 ( 44) SS BOND : angle 0.94844 ( 88) hydrogen bonds : bond 0.03890 ( 1118) hydrogen bonds : angle 5.13927 ( 3069) link_BETA1-4 : bond 0.00480 ( 18) link_BETA1-4 : angle 1.65628 ( 54) link_NAG-ASN : bond 0.00431 ( 48) link_NAG-ASN : angle 2.76482 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 280 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8959 (p) cc_final: 0.8659 (t) REVERT: A 869 MET cc_start: 0.8934 (mtt) cc_final: 0.8514 (mtm) REVERT: A 979 ASP cc_start: 0.8764 (t70) cc_final: 0.8375 (t0) REVERT: B 505 TYR cc_start: 0.5767 (t80) cc_final: 0.5341 (t80) REVERT: B 966 LEU cc_start: 0.9624 (OUTLIER) cc_final: 0.9228 (mp) REVERT: C 153 MET cc_start: 0.4461 (ppp) cc_final: 0.3489 (tmm) REVERT: C 584 ILE cc_start: 0.8793 (mm) cc_final: 0.8243 (mm) REVERT: C 796 ASP cc_start: 0.8019 (p0) cc_final: 0.7498 (p0) REVERT: C 935 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8134 (tm-30) REVERT: D 81 GLU cc_start: 0.8842 (pp20) cc_final: 0.8413 (pp20) REVERT: E 76 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8682 (tmmt) REVERT: E 87 ARG cc_start: 0.7512 (ptp-110) cc_final: 0.7134 (ptp-110) REVERT: E 99 ASP cc_start: 0.8971 (t70) cc_final: 0.8646 (t0) REVERT: E 111 ASP cc_start: 0.8625 (t0) cc_final: 0.8346 (t0) REVERT: E 112 TYR cc_start: 0.8618 (m-80) cc_final: 0.8266 (m-80) REVERT: H 39 LYS cc_start: 0.8582 (tppt) cc_final: 0.8188 (mmtp) REVERT: H 47 LEU cc_start: 0.8902 (mm) cc_final: 0.8584 (mm) REVERT: H 49 TYR cc_start: 0.7997 (p90) cc_final: 0.7686 (p90) REVERT: H 87 TYR cc_start: 0.7663 (m-80) cc_final: 0.7290 (m-10) REVERT: I 46 GLU cc_start: 0.7912 (tt0) cc_final: 0.7542 (pt0) REVERT: F 45 LYS cc_start: 0.8942 (tppt) cc_final: 0.8735 (tppt) REVERT: G 29 PHE cc_start: 0.7554 (t80) cc_final: 0.7067 (t80) REVERT: G 53 TRP cc_start: 0.8981 (p-90) cc_final: 0.8482 (p-90) REVERT: G 104 ILE cc_start: 0.8179 (tp) cc_final: 0.7811 (mm) REVERT: J 4 MET cc_start: 0.7071 (mtp) cc_final: 0.6389 (ttm) REVERT: K 47 TRP cc_start: 0.3884 (t60) cc_final: 0.3315 (t60) REVERT: K 82 GLN cc_start: 0.4670 (mm110) cc_final: 0.4303 (mm-40) REVERT: K 84 ASN cc_start: 0.8022 (m110) cc_final: 0.7301 (p0) REVERT: K 98 LYS cc_start: 0.5342 (ptmm) cc_final: 0.4905 (tptm) outliers start: 69 outliers final: 44 residues processed: 330 average time/residue: 0.1925 time to fit residues: 104.5659 Evaluate side-chains 309 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 262 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 83 PHE Chi-restraints excluded: chain F residue 88 CYS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 95 TYR Chi-restraints excluded: chain K residue 110 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 396 optimal weight: 0.0980 chunk 359 optimal weight: 8.9990 chunk 372 optimal weight: 30.0000 chunk 120 optimal weight: 1.9990 chunk 232 optimal weight: 5.9990 chunk 376 optimal weight: 0.8980 chunk 317 optimal weight: 3.9990 chunk 160 optimal weight: 0.9980 chunk 308 optimal weight: 0.9990 chunk 244 optimal weight: 0.7980 chunk 205 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 89 GLN ** K 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.103690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.065311 restraints weight = 83172.614| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.77 r_work: 0.2890 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 33041 Z= 0.105 Angle : 0.553 12.032 45100 Z= 0.274 Chirality : 0.044 0.435 5244 Planarity : 0.003 0.052 5715 Dihedral : 4.932 49.501 5732 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.21 % Allowed : 13.50 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.13), residues: 3986 helix: 2.29 (0.22), residues: 654 sheet: 0.25 (0.16), residues: 1062 loop : -1.21 (0.12), residues: 2270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 100 TYR 0.019 0.001 TYR B1067 PHE 0.012 0.001 PHE F 36 TRP 0.035 0.001 TRP K 113 HIS 0.008 0.001 HIS J 38 Details of bonding type rmsd covalent geometry : bond 0.00243 (32931) covalent geometry : angle 0.52780 (44814) SS BOND : bond 0.00212 ( 44) SS BOND : angle 0.98407 ( 88) hydrogen bonds : bond 0.03795 ( 1118) hydrogen bonds : angle 5.01033 ( 3069) link_BETA1-4 : bond 0.00460 ( 18) link_BETA1-4 : angle 1.65409 ( 54) link_NAG-ASN : bond 0.00414 ( 48) link_NAG-ASN : angle 2.71295 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 274 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8960 (p) cc_final: 0.8638 (t) REVERT: A 869 MET cc_start: 0.8933 (mtt) cc_final: 0.8521 (mtm) REVERT: A 979 ASP cc_start: 0.8777 (t70) cc_final: 0.8378 (t0) REVERT: B 52 GLN cc_start: 0.9051 (tt0) cc_final: 0.8819 (tm-30) REVERT: B 451 TYR cc_start: 0.7326 (m-80) cc_final: 0.7114 (m-80) REVERT: B 505 TYR cc_start: 0.5820 (t80) cc_final: 0.5555 (t80) REVERT: B 614 ASP cc_start: 0.8551 (t70) cc_final: 0.8204 (t0) REVERT: B 966 LEU cc_start: 0.9630 (OUTLIER) cc_final: 0.9252 (mp) REVERT: C 153 MET cc_start: 0.4461 (ppp) cc_final: 0.3492 (tmm) REVERT: C 584 ILE cc_start: 0.8776 (mm) cc_final: 0.8195 (mm) REVERT: C 796 ASP cc_start: 0.8024 (p0) cc_final: 0.7580 (p0) REVERT: C 935 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8150 (tm-30) REVERT: D 81 GLU cc_start: 0.8840 (pp20) cc_final: 0.8392 (pp20) REVERT: E 87 ARG cc_start: 0.7379 (ptp-110) cc_final: 0.6983 (ptp-110) REVERT: E 99 ASP cc_start: 0.8978 (t70) cc_final: 0.8672 (t0) REVERT: E 111 ASP cc_start: 0.8634 (t0) cc_final: 0.8364 (t0) REVERT: H 4 MET cc_start: 0.7686 (mmm) cc_final: 0.7398 (tpp) REVERT: H 37 GLN cc_start: 0.8745 (tt0) cc_final: 0.7987 (tt0) REVERT: H 39 LYS cc_start: 0.8585 (tppt) cc_final: 0.8218 (mmtp) REVERT: H 47 LEU cc_start: 0.8874 (mm) cc_final: 0.8492 (mm) REVERT: H 49 TYR cc_start: 0.7976 (p90) cc_final: 0.7730 (p90) REVERT: H 62 PHE cc_start: 0.8612 (m-10) cc_final: 0.8394 (m-10) REVERT: H 87 TYR cc_start: 0.7708 (m-80) cc_final: 0.7358 (m-10) REVERT: I 46 GLU cc_start: 0.7912 (tt0) cc_final: 0.7538 (pt0) REVERT: F 39 LYS cc_start: 0.8815 (mmmt) cc_final: 0.8595 (mmtm) REVERT: F 83 PHE cc_start: 0.7969 (OUTLIER) cc_final: 0.7402 (m-80) REVERT: G 29 PHE cc_start: 0.7524 (t80) cc_final: 0.7003 (t80) REVERT: G 100 ARG cc_start: 0.7546 (ttm110) cc_final: 0.7157 (ttm110) REVERT: G 104 ILE cc_start: 0.8144 (tp) cc_final: 0.7748 (mm) REVERT: J 4 MET cc_start: 0.6949 (mtp) cc_final: 0.6013 (ttm) REVERT: J 89 GLN cc_start: 0.3938 (tm-30) cc_final: 0.3622 (tm-30) REVERT: K 47 TRP cc_start: 0.4037 (t60) cc_final: 0.3513 (t60) REVERT: K 82 GLN cc_start: 0.4592 (mm110) cc_final: 0.4367 (mm-40) REVERT: K 84 ASN cc_start: 0.8094 (m110) cc_final: 0.7497 (p0) REVERT: K 98 LYS cc_start: 0.5874 (ptmm) cc_final: 0.5301 (tptm) outliers start: 76 outliers final: 54 residues processed: 331 average time/residue: 0.1917 time to fit residues: 104.4379 Evaluate side-chains 316 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 259 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 83 PHE Chi-restraints excluded: chain F residue 88 CYS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 110 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 20 optimal weight: 8.9990 chunk 299 optimal weight: 0.9990 chunk 219 optimal weight: 7.9990 chunk 176 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 332 optimal weight: 0.9980 chunk 230 optimal weight: 7.9990 chunk 396 optimal weight: 20.0000 chunk 302 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN B 81 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.102716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.064179 restraints weight = 84044.843| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.79 r_work: 0.2862 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33041 Z= 0.140 Angle : 0.571 12.343 45100 Z= 0.285 Chirality : 0.045 0.438 5244 Planarity : 0.003 0.055 5715 Dihedral : 4.739 43.272 5732 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.30 % Allowed : 13.94 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.13), residues: 3986 helix: 2.23 (0.22), residues: 657 sheet: 0.27 (0.16), residues: 1081 loop : -1.25 (0.12), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 16 TYR 0.024 0.001 TYR J 86 PHE 0.013 0.001 PHE B 86 TRP 0.041 0.001 TRP K 113 HIS 0.014 0.001 HIS J 38 Details of bonding type rmsd covalent geometry : bond 0.00331 (32931) covalent geometry : angle 0.54702 (44814) SS BOND : bond 0.00248 ( 44) SS BOND : angle 1.01790 ( 88) hydrogen bonds : bond 0.04071 ( 1118) hydrogen bonds : angle 4.98101 ( 3069) link_BETA1-4 : bond 0.00478 ( 18) link_BETA1-4 : angle 1.66503 ( 54) link_NAG-ASN : bond 0.00389 ( 48) link_NAG-ASN : angle 2.71203 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 276 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.9061 (p) cc_final: 0.8759 (t) REVERT: A 869 MET cc_start: 0.8986 (mtt) cc_final: 0.8587 (mtm) REVERT: A 979 ASP cc_start: 0.8779 (t70) cc_final: 0.8370 (t0) REVERT: B 52 GLN cc_start: 0.9064 (tt0) cc_final: 0.8813 (tm-30) REVERT: B 451 TYR cc_start: 0.7339 (m-80) cc_final: 0.7118 (m-80) REVERT: B 505 TYR cc_start: 0.5871 (t80) cc_final: 0.5553 (t80) REVERT: B 614 ASP cc_start: 0.8564 (t70) cc_final: 0.8214 (t0) REVERT: B 966 LEU cc_start: 0.9654 (OUTLIER) cc_final: 0.9270 (mp) REVERT: C 153 MET cc_start: 0.4502 (ppp) cc_final: 0.3534 (tmm) REVERT: C 584 ILE cc_start: 0.8787 (mm) cc_final: 0.8213 (mm) REVERT: C 796 ASP cc_start: 0.8045 (p0) cc_final: 0.7591 (p0) REVERT: C 935 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8260 (tm-30) REVERT: D 42 LYS cc_start: 0.8988 (mtmm) cc_final: 0.8672 (mtmm) REVERT: D 81 GLU cc_start: 0.8838 (pp20) cc_final: 0.8339 (pp20) REVERT: E 80 TYR cc_start: 0.9057 (m-80) cc_final: 0.8845 (m-80) REVERT: E 87 ARG cc_start: 0.7415 (ptp-110) cc_final: 0.6893 (ptp-110) REVERT: E 99 ASP cc_start: 0.9032 (t70) cc_final: 0.8752 (t0) REVERT: E 111 ASP cc_start: 0.8652 (t0) cc_final: 0.8316 (t0) REVERT: E 112 TYR cc_start: 0.8642 (m-80) cc_final: 0.8196 (m-80) REVERT: H 4 MET cc_start: 0.7767 (mmm) cc_final: 0.7505 (tpp) REVERT: H 37 GLN cc_start: 0.8695 (tt0) cc_final: 0.8345 (tt0) REVERT: H 39 LYS cc_start: 0.8658 (tppt) cc_final: 0.8364 (mmtp) REVERT: H 47 LEU cc_start: 0.8928 (mm) cc_final: 0.8552 (mm) REVERT: H 49 TYR cc_start: 0.8076 (p90) cc_final: 0.7803 (p90) REVERT: H 85 THR cc_start: 0.7168 (OUTLIER) cc_final: 0.6891 (p) REVERT: H 87 TYR cc_start: 0.7739 (m-80) cc_final: 0.7320 (m-10) REVERT: I 46 GLU cc_start: 0.7937 (tt0) cc_final: 0.7567 (pt0) REVERT: F 83 PHE cc_start: 0.8020 (OUTLIER) cc_final: 0.7429 (m-80) REVERT: G 16 ARG cc_start: 0.6816 (ttp-110) cc_final: 0.5953 (ptt180) REVERT: G 29 PHE cc_start: 0.7756 (t80) cc_final: 0.7228 (t80) REVERT: G 95 TYR cc_start: 0.6422 (OUTLIER) cc_final: 0.5001 (m-80) REVERT: G 100 ARG cc_start: 0.7629 (ttm110) cc_final: 0.7244 (ttm110) REVERT: G 104 ILE cc_start: 0.8177 (tp) cc_final: 0.7775 (mm) REVERT: G 112 TYR cc_start: 0.8663 (OUTLIER) cc_final: 0.8077 (m-10) REVERT: J 4 MET cc_start: 0.6657 (mtp) cc_final: 0.5546 (ttm) REVERT: J 89 GLN cc_start: 0.3879 (tm-30) cc_final: 0.3672 (tm-30) REVERT: K 47 TRP cc_start: 0.4208 (t60) cc_final: 0.3750 (t60) REVERT: K 84 ASN cc_start: 0.8135 (m110) cc_final: 0.7585 (p0) REVERT: K 98 LYS cc_start: 0.5870 (ptmm) cc_final: 0.5338 (tptt) outliers start: 79 outliers final: 60 residues processed: 335 average time/residue: 0.1877 time to fit residues: 104.0273 Evaluate side-chains 329 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 263 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 84 ASN Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 83 PHE Chi-restraints excluded: chain F residue 88 CYS Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 95 TYR Chi-restraints excluded: chain G residue 112 TYR Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain K residue 110 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 88 optimal weight: 2.9990 chunk 259 optimal weight: 8.9990 chunk 114 optimal weight: 8.9990 chunk 342 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 284 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 322 optimal weight: 0.5980 chunk 327 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.103023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.064555 restraints weight = 84152.944| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.78 r_work: 0.2871 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33041 Z= 0.119 Angle : 0.569 12.152 45100 Z= 0.282 Chirality : 0.044 0.435 5244 Planarity : 0.003 0.053 5715 Dihedral : 4.560 37.473 5732 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.18 % Allowed : 14.17 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.13), residues: 3986 helix: 2.30 (0.22), residues: 656 sheet: 0.27 (0.16), residues: 1096 loop : -1.22 (0.12), residues: 2234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 24 TYR 0.031 0.001 TYR J 87 PHE 0.013 0.001 PHE D 83 TRP 0.047 0.001 TRP K 113 HIS 0.029 0.001 HIS J 38 Details of bonding type rmsd covalent geometry : bond 0.00277 (32931) covalent geometry : angle 0.54547 (44814) SS BOND : bond 0.00214 ( 44) SS BOND : angle 0.98075 ( 88) hydrogen bonds : bond 0.03896 ( 1118) hydrogen bonds : angle 4.90389 ( 3069) link_BETA1-4 : bond 0.00463 ( 18) link_BETA1-4 : angle 1.67913 ( 54) link_NAG-ASN : bond 0.00396 ( 48) link_NAG-ASN : angle 2.66374 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 274 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.9066 (p) cc_final: 0.8757 (t) REVERT: A 869 MET cc_start: 0.8976 (mtt) cc_final: 0.8581 (mtm) REVERT: A 979 ASP cc_start: 0.8765 (t70) cc_final: 0.8353 (t0) REVERT: B 52 GLN cc_start: 0.9064 (tt0) cc_final: 0.8792 (tm-30) REVERT: B 505 TYR cc_start: 0.5938 (t80) cc_final: 0.5624 (t80) REVERT: B 614 ASP cc_start: 0.8541 (t70) cc_final: 0.8194 (t0) REVERT: B 966 LEU cc_start: 0.9650 (OUTLIER) cc_final: 0.9278 (mp) REVERT: C 153 MET cc_start: 0.4571 (ppp) cc_final: 0.3573 (tmm) REVERT: C 396 TYR cc_start: 0.8170 (m-80) cc_final: 0.7839 (m-80) REVERT: C 584 ILE cc_start: 0.8765 (mm) cc_final: 0.8184 (mm) REVERT: C 796 ASP cc_start: 0.8040 (p0) cc_final: 0.7590 (p0) REVERT: C 935 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8297 (tm-30) REVERT: D 42 LYS cc_start: 0.8996 (mtmm) cc_final: 0.8687 (mtmm) REVERT: D 81 GLU cc_start: 0.8853 (pp20) cc_final: 0.8349 (pp20) REVERT: E 87 ARG cc_start: 0.7424 (ptp-110) cc_final: 0.7141 (ptp-110) REVERT: E 89 GLU cc_start: 0.8179 (pm20) cc_final: 0.7949 (pm20) REVERT: E 99 ASP cc_start: 0.9017 (t70) cc_final: 0.8717 (t0) REVERT: E 111 ASP cc_start: 0.8616 (t0) cc_final: 0.8238 (t0) REVERT: E 112 TYR cc_start: 0.8648 (m-80) cc_final: 0.8156 (m-80) REVERT: H 37 GLN cc_start: 0.8730 (tt0) cc_final: 0.8331 (tt0) REVERT: H 39 LYS cc_start: 0.8645 (tppt) cc_final: 0.8088 (mmtp) REVERT: H 47 LEU cc_start: 0.8890 (mm) cc_final: 0.8522 (mm) REVERT: H 49 TYR cc_start: 0.8049 (p90) cc_final: 0.7806 (p90) REVERT: H 82 ASP cc_start: 0.7405 (p0) cc_final: 0.7162 (p0) REVERT: H 85 THR cc_start: 0.7234 (OUTLIER) cc_final: 0.6977 (p) REVERT: H 87 TYR cc_start: 0.7781 (m-80) cc_final: 0.7331 (m-10) REVERT: I 46 GLU cc_start: 0.7946 (tt0) cc_final: 0.7592 (pt0) REVERT: G 16 ARG cc_start: 0.6990 (ttp-110) cc_final: 0.6220 (ptt180) REVERT: G 29 PHE cc_start: 0.7798 (t80) cc_final: 0.7260 (t80) REVERT: G 95 TYR cc_start: 0.6413 (OUTLIER) cc_final: 0.5051 (m-80) REVERT: G 104 ILE cc_start: 0.8144 (tp) cc_final: 0.7708 (mm) REVERT: G 112 TYR cc_start: 0.8688 (OUTLIER) cc_final: 0.8126 (m-10) REVERT: K 47 TRP cc_start: 0.4162 (t60) cc_final: 0.3749 (t60) REVERT: K 84 ASN cc_start: 0.8194 (m110) cc_final: 0.7656 (p0) REVERT: K 98 LYS cc_start: 0.5825 (ptmm) cc_final: 0.5337 (tptt) outliers start: 75 outliers final: 59 residues processed: 330 average time/residue: 0.1886 time to fit residues: 102.3968 Evaluate side-chains 327 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 263 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 88 CYS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 95 TYR Chi-restraints excluded: chain G residue 112 TYR Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain K residue 110 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 302 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 189 optimal weight: 0.6980 chunk 343 optimal weight: 20.0000 chunk 159 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 chunk 396 optimal weight: 20.0000 chunk 44 optimal weight: 0.8980 chunk 370 optimal weight: 0.6980 chunk 364 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1002 GLN F 3 GLN J 89 GLN ** K 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.103323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.064979 restraints weight = 83282.443| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 3.78 r_work: 0.2880 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 33041 Z= 0.111 Angle : 0.569 11.957 45100 Z= 0.283 Chirality : 0.044 0.435 5244 Planarity : 0.003 0.058 5715 Dihedral : 4.412 34.800 5732 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.04 % Allowed : 14.52 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.13), residues: 3986 helix: 2.32 (0.22), residues: 654 sheet: 0.29 (0.16), residues: 1082 loop : -1.16 (0.12), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 16 TYR 0.019 0.001 TYR B1067 PHE 0.012 0.001 PHE F 36 TRP 0.041 0.001 TRP K 113 HIS 0.028 0.001 HIS J 38 Details of bonding type rmsd covalent geometry : bond 0.00258 (32931) covalent geometry : angle 0.54671 (44814) SS BOND : bond 0.00209 ( 44) SS BOND : angle 0.92530 ( 88) hydrogen bonds : bond 0.03797 ( 1118) hydrogen bonds : angle 4.85689 ( 3069) link_BETA1-4 : bond 0.00436 ( 18) link_BETA1-4 : angle 1.67837 ( 54) link_NAG-ASN : bond 0.00398 ( 48) link_NAG-ASN : angle 2.62137 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 276 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.9052 (p) cc_final: 0.8735 (t) REVERT: A 869 MET cc_start: 0.8959 (mtt) cc_final: 0.8558 (mtm) REVERT: A 979 ASP cc_start: 0.8735 (t70) cc_final: 0.8316 (t0) REVERT: A 1019 ARG cc_start: 0.8557 (ttp80) cc_final: 0.8107 (tpt170) REVERT: B 52 GLN cc_start: 0.9055 (tt0) cc_final: 0.8781 (tm-30) REVERT: B 505 TYR cc_start: 0.5918 (t80) cc_final: 0.5582 (t80) REVERT: B 614 ASP cc_start: 0.8540 (t70) cc_final: 0.8205 (t0) REVERT: B 966 LEU cc_start: 0.9650 (OUTLIER) cc_final: 0.9288 (mp) REVERT: C 153 MET cc_start: 0.4536 (ppp) cc_final: 0.3534 (tmm) REVERT: C 269 TYR cc_start: 0.8321 (m-80) cc_final: 0.7894 (m-80) REVERT: C 396 TYR cc_start: 0.8197 (m-80) cc_final: 0.7887 (m-80) REVERT: C 584 ILE cc_start: 0.8743 (mm) cc_final: 0.8162 (mm) REVERT: C 796 ASP cc_start: 0.8019 (p0) cc_final: 0.7576 (p0) REVERT: C 935 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8292 (tm-30) REVERT: D 42 LYS cc_start: 0.8988 (mtmm) cc_final: 0.8684 (mtmm) REVERT: D 81 GLU cc_start: 0.8836 (pp20) cc_final: 0.8343 (pp20) REVERT: E 87 ARG cc_start: 0.7434 (ptp-110) cc_final: 0.7131 (ptp-110) REVERT: E 89 GLU cc_start: 0.8191 (pm20) cc_final: 0.7927 (pm20) REVERT: E 99 ASP cc_start: 0.9012 (t70) cc_final: 0.8716 (t0) REVERT: E 111 ASP cc_start: 0.8651 (t0) cc_final: 0.8254 (t0) REVERT: E 112 TYR cc_start: 0.8639 (m-80) cc_final: 0.8114 (m-80) REVERT: H 37 GLN cc_start: 0.8665 (tt0) cc_final: 0.8342 (tt0) REVERT: H 39 LYS cc_start: 0.8632 (tppt) cc_final: 0.8282 (mmtp) REVERT: H 47 LEU cc_start: 0.8886 (mm) cc_final: 0.8511 (mm) REVERT: H 49 TYR cc_start: 0.8044 (p90) cc_final: 0.7816 (p90) REVERT: H 85 THR cc_start: 0.7195 (OUTLIER) cc_final: 0.6913 (p) REVERT: H 87 TYR cc_start: 0.7783 (m-80) cc_final: 0.7365 (m-10) REVERT: I 46 GLU cc_start: 0.7914 (tt0) cc_final: 0.7569 (pt0) REVERT: G 16 ARG cc_start: 0.7113 (ttp-110) cc_final: 0.6266 (ptt180) REVERT: G 29 PHE cc_start: 0.7855 (t80) cc_final: 0.7312 (t80) REVERT: G 95 TYR cc_start: 0.6446 (OUTLIER) cc_final: 0.5115 (m-80) REVERT: G 104 ILE cc_start: 0.8103 (tp) cc_final: 0.7689 (mm) REVERT: K 84 ASN cc_start: 0.8226 (m110) cc_final: 0.7695 (p0) REVERT: K 98 LYS cc_start: 0.5777 (ptmm) cc_final: 0.5307 (tptt) outliers start: 70 outliers final: 58 residues processed: 328 average time/residue: 0.1869 time to fit residues: 100.2159 Evaluate side-chains 327 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 265 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 88 CYS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 95 TYR Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain K residue 110 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 232 optimal weight: 2.9990 chunk 322 optimal weight: 0.0070 chunk 231 optimal weight: 0.8980 chunk 364 optimal weight: 7.9990 chunk 332 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 372 optimal weight: 20.0000 chunk 250 optimal weight: 0.5980 chunk 296 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 overall best weight: 1.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.102114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.063642 restraints weight = 84280.813| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.80 r_work: 0.2852 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 33041 Z= 0.149 Angle : 0.593 12.279 45100 Z= 0.296 Chirality : 0.045 0.442 5244 Planarity : 0.004 0.055 5715 Dihedral : 4.422 32.239 5732 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.86 % Allowed : 14.87 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.13), residues: 3986 helix: 2.24 (0.22), residues: 658 sheet: 0.23 (0.16), residues: 1096 loop : -1.22 (0.12), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 16 TYR 0.020 0.001 TYR J 86 PHE 0.022 0.001 PHE I 68 TRP 0.037 0.001 TRP K 113 HIS 0.016 0.001 HIS J 38 Details of bonding type rmsd covalent geometry : bond 0.00354 (32931) covalent geometry : angle 0.57001 (44814) SS BOND : bond 0.00243 ( 44) SS BOND : angle 1.11026 ( 88) hydrogen bonds : bond 0.04175 ( 1118) hydrogen bonds : angle 4.91824 ( 3069) link_BETA1-4 : bond 0.00408 ( 18) link_BETA1-4 : angle 1.68685 ( 54) link_NAG-ASN : bond 0.00374 ( 48) link_NAG-ASN : angle 2.64940 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 273 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.9060 (p) cc_final: 0.8742 (t) REVERT: A 869 MET cc_start: 0.9033 (mtt) cc_final: 0.8645 (mtm) REVERT: A 979 ASP cc_start: 0.8785 (t70) cc_final: 0.8347 (t0) REVERT: B 52 GLN cc_start: 0.9083 (tt0) cc_final: 0.8793 (tm-30) REVERT: B 505 TYR cc_start: 0.6014 (t80) cc_final: 0.5674 (t80) REVERT: B 614 ASP cc_start: 0.8540 (t70) cc_final: 0.8190 (t0) REVERT: B 966 LEU cc_start: 0.9659 (OUTLIER) cc_final: 0.9282 (mp) REVERT: C 153 MET cc_start: 0.4595 (ppp) cc_final: 0.3663 (tmm) REVERT: C 269 TYR cc_start: 0.8317 (m-80) cc_final: 0.7893 (m-80) REVERT: C 584 ILE cc_start: 0.8776 (mm) cc_final: 0.8198 (mm) REVERT: C 796 ASP cc_start: 0.8026 (p0) cc_final: 0.7577 (p0) REVERT: C 935 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8333 (tm-30) REVERT: D 42 LYS cc_start: 0.9023 (mtmm) cc_final: 0.8713 (mtmm) REVERT: D 81 GLU cc_start: 0.8826 (pp20) cc_final: 0.8289 (pp20) REVERT: E 87 ARG cc_start: 0.7552 (ptp-110) cc_final: 0.7264 (ptp-110) REVERT: E 89 GLU cc_start: 0.8235 (pm20) cc_final: 0.7953 (pm20) REVERT: E 99 ASP cc_start: 0.9102 (t70) cc_final: 0.8829 (t0) REVERT: E 111 ASP cc_start: 0.8615 (t0) cc_final: 0.8215 (t0) REVERT: E 112 TYR cc_start: 0.8714 (m-80) cc_final: 0.8186 (m-80) REVERT: H 37 GLN cc_start: 0.8685 (tt0) cc_final: 0.8346 (tt0) REVERT: H 39 LYS cc_start: 0.8663 (tppt) cc_final: 0.8311 (mmtp) REVERT: H 47 LEU cc_start: 0.8889 (mm) cc_final: 0.8501 (mm) REVERT: H 49 TYR cc_start: 0.8116 (p90) cc_final: 0.7888 (p90) REVERT: H 85 THR cc_start: 0.7137 (OUTLIER) cc_final: 0.6864 (p) REVERT: H 87 TYR cc_start: 0.7869 (m-80) cc_final: 0.7464 (m-10) REVERT: I 46 GLU cc_start: 0.7944 (tt0) cc_final: 0.7637 (pt0) REVERT: G 16 ARG cc_start: 0.7214 (ttp-110) cc_final: 0.6379 (ptt180) REVERT: G 29 PHE cc_start: 0.8003 (t80) cc_final: 0.7445 (t80) REVERT: G 48 VAL cc_start: 0.8451 (t) cc_final: 0.8209 (p) REVERT: G 95 TYR cc_start: 0.6341 (OUTLIER) cc_final: 0.4969 (m-80) REVERT: G 104 ILE cc_start: 0.8124 (tp) cc_final: 0.7699 (mm) REVERT: J 70 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.6828 (m-30) REVERT: K 39 GLN cc_start: 0.7382 (tp40) cc_final: 0.7032 (tp-100) REVERT: K 80 TYR cc_start: 0.8085 (OUTLIER) cc_final: 0.6845 (m-80) REVERT: K 98 LYS cc_start: 0.5853 (ptmm) cc_final: 0.5407 (tptt) outliers start: 64 outliers final: 53 residues processed: 320 average time/residue: 0.1975 time to fit residues: 103.6687 Evaluate side-chains 329 residues out of total 3514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 270 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 88 CYS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 95 TYR Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain K residue 80 TYR Chi-restraints excluded: chain K residue 110 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 127 optimal weight: 0.2980 chunk 291 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 203 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 345 optimal weight: 5.9990 chunk 115 optimal weight: 0.7980 chunk 373 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN C1002 GLN F 3 GLN ** K 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.102094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.063654 restraints weight = 84184.054| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 3.80 r_work: 0.2852 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33041 Z= 0.141 Angle : 0.583 12.253 45100 Z= 0.291 Chirality : 0.045 0.445 5244 Planarity : 0.003 0.055 5715 Dihedral : 4.391 31.546 5732 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.98 % Allowed : 15.01 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.13), residues: 3986 helix: 2.21 (0.22), residues: 659 sheet: 0.22 (0.15), residues: 1098 loop : -1.21 (0.12), residues: 2229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 16 TYR 0.019 0.001 TYR B1067 PHE 0.016 0.001 PHE F 36 TRP 0.035 0.001 TRP K 113 HIS 0.010 0.001 HIS J 38 Details of bonding type rmsd covalent geometry : bond 0.00336 (32931) covalent geometry : angle 0.56050 (44814) SS BOND : bond 0.00240 ( 44) SS BOND : angle 1.06668 ( 88) hydrogen bonds : bond 0.04123 ( 1118) hydrogen bonds : angle 4.88633 ( 3069) link_BETA1-4 : bond 0.00411 ( 18) link_BETA1-4 : angle 1.69917 ( 54) link_NAG-ASN : bond 0.00371 ( 48) link_NAG-ASN : angle 2.61166 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8980.89 seconds wall clock time: 154 minutes 16.43 seconds (9256.43 seconds total)